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Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.
- Source :
-
F1000Research [F1000Res] 2016 May 20; Vol. 5, pp. 950. Date of Electronic Publication: 2016 May 20 (Print Publication: 2016). - Publication Year :
- 2016
-
Abstract
- The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C). These genome-wide experiments generate large amounts of data that require careful analysis to obtain useful biological conclusions. However, development of the appropriate software tools is hindered by the lack of basic infrastructure to represent and manipulate genomic interaction data. Here, we present the InteractionSet package that provides classes to represent genomic interactions and store their associated experimental data, along with the methods required for low-level manipulation and processing of those classes. The InteractionSet package exploits existing infrastructure in the open-source Bioconductor project, while in turn being used by Bioconductor packages designed for higher-level analyses. For new packages, use of the functionality in InteractionSet will simplify development, allow access to more features and improve interoperability between packages.
Details
- Language :
- English
- ISSN :
- 2046-1402
- Volume :
- 5
- Database :
- MEDLINE
- Journal :
- F1000Research
- Publication Type :
- Academic Journal
- Accession number :
- 27303634.2
- Full Text :
- https://doi.org/10.12688/f1000research.8759.2